A critical measure of the genetic architecture of a phenotype is the effect size of a locus, by which we mean the extent to which a locus contributes to the variance of a phenotype or, as in the case here when disease outcome is involved, the extent to which it increases the risk of disease susceptibility. The power to detect an allele with a given relative risk depends on the size of the odds ratio, or percentage of phenotypic variance explained, and also on the allele frequency. For a locus with two alleles, power to detect is maximal when the allele frequency is 0·5 and the relative risk is large. This is the characteristic we expect to find at loci that contribute to disease susceptibility in a genetically tractable phenotype.
